Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 208249 DVU2743 high-affinity branched-chain amino acid ABC ransporter, permease protein
Query= uniprot:Q1MCU0 (300 letters) >MicrobesOnline__882:208249 Length = 306 Score = 213 bits (542), Expect = 4e-60 Identities = 121/308 (39%), Positives = 180/308 (58%), Gaps = 10/308 (3%) Query: 1 MEYFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSI 60 ME F+Q + N L GS Y L+A+GYT+VYG++ +INFAHGDIFM+G + + V +L Sbjct: 1 METFIQNIFNALQWGSFYALIALGYTLVYGVLLLINFAHGDIFMVGAYISFFVASILLGQ 60 Query: 61 FAGL-----PVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLR--GSFRLAPLITAIGMSI 113 G P+A+ L V L M++T+ T+ERVAYRPLR G+ RL +ITA+ I Sbjct: 61 IGGFFELSGPMALALTVPLT--MVLTAGVGVTLERVAYRPLRRKGAHRLYVVITALMCGI 118 Query: 114 TLSNFIQVTQGPRNKPIPPMVSSV-YQFGNISVSLKQIIIIVITAVLLTIFWYIVNRTAL 172 L N G K +P M+ V Y G +SV+ ++++IV ++ + +IV RT + Sbjct: 119 MLENGNLALLGASRKALPEMIDKVVYTIGTVSVTNLKLMVIVTAFLVFALLQFIVTRTRI 178 Query: 173 GRAQRATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGV 232 G A RA D+ L+G+ +D I TFV+G+ A +AG ++ M Y + G G Sbjct: 179 GMAMRAVAWDKFALPLMGIPLDSIIVFTFVLGSGFAGLAGLLFAMSYPILDPYMGAMVGW 238 Query: 233 KAFTAAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGIL 292 KAF AAV+GGIG + GA GG L+ IE + +A F ++D+ F+IL F++ +PTG+ Sbjct: 239 KAFIAAVVGGIGDIRGAFIGGFLLAFIEIMVAAVFPSTFRDLFAFSILLFIMWQRPTGLF 298 Query: 293 GRPEVEKV 300 G + K+ Sbjct: 299 GVAKTTKI 306 Lambda K H 0.329 0.143 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 281 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 300 Length of database: 306 Length adjustment: 27 Effective length of query: 273 Effective length of database: 279 Effective search space: 76167 Effective search space used: 76167 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory